Non-contiguous finished genome sequence and description of Kurthia senegalensis sp. nov

Standards in Genomic Sciences

Volumn 9, Issue 3, 2015, Pages 1319-1230

  Roux, Véronique ^a   Lagier, Jean Christophe ^a   Gorlas, Aurore ^a   Robert, Catherine ^a   Raoult, Didier ^a  

^a AIX MARSEILLE UNIVERSITY   (France)

Author keywords

Capsule; Culturomics; Firmicutes; Flagella; Kurthia senegalensis

Indexed keywords

AMOXICILLIN PLUS CLAVULANIC ACID; CEFTRIAXONE; CIPROFLOXACIN; COTRIMOXAZOLE; DNA 16S; DOXYCYCLINE; ERYTHROMYCIN; GENTAMICIN; IMIPENEM; METRONIDAZOLE; NITROFURANTOIN; PENICILLIN G; RIFAMPICIN; RNA 16S; VANCOMYCIN;

ADOLESCENT; AEROBIC BACTERIUM; ANTIBIOTIC RESISTANCE; ANTIBIOTIC SENSITIVITY; ARTICLE; BACTERIAL CAPSULE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIUM COLONY; CONTROLLED STUDY; FIRMICUTES; GENE SEQUENCE; GENOME ANALYSIS; GENOME SIZE; GENOMICS; GRAM POSITIVE BACTERIUM; HUMAN; KURTHIA SENEGALENSIS; MALE; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; PROPHAGE; PROTEIN ANALYSIS; RNA GENE; TRANSMISSION ELECTRON MICROSCOPY;

EID: 84954150046     PISSN: None     EISSN: 19443277     Source Type: Journal    
DOI: 10.4056/sigs.5078947     Document Type: Article

References (43)

1. Lagier JC, Armougom F, Million M, Hugon P, Pagnier I, Robert C, Bittar F, Fournous G, Gimenez G, Maraninchi M, et al. Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect 2012; 18:1185-1193. PubMed
2. Rossello-Mora R. DNA-DNA reassociation methods applied to microbial taxonomy and their critical evaluation. In: Stackebrandt E (ed), Molecular Identification, Systematics, and population Structure of Prokaryotes, Springer, Berlin, 2006, p. 23-50.
3. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463-464. http://dx.doi.org/10.1099/00207713-37-4-463
4. Tindall BJ, Rossello-Mora R, Busse HJ, Ludwig W, Kämpfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010; 60:249-266. PubMed http://dx.doi.org/10.1099/ijs.0.016949-0
5. Auch AF, Klenk HP, Göker M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2010; 2:142-148. PubMed http://dx.doi.org/10.4056/sigs.541628
6. Trevisan V. Caretteri di alcuni nuovi generi di Batteriacee. Atti della Accademia Fisio-Medico-Statistica in Milano, Series 4 1985; 3:92-107.
7. Breed RS, Murray EGD, Smith NR, eds. Bergey's Manual of Determinative Bacteriology, 7th ed. Williams and Wilkins. Baltimore, MD. 1957.
8. Keddie RM, Shaw S. Genus Kurthia. In: Sneath PHA, Mair NS, Sharpe ME and Holt JG (Eds.) Bergey's Manual of Systematic Bacteriology. Volume 2, The Williams and Wilkins Co., Baltimore,1986, p. 1255-1258.
9. Belikova VA, Cherevach NV, Kalakutskii LV. A new species of bacteria of the genus Kurthia, Kurthia sibirica sp. nov. Mikrobiologiia 1986; 55:831-835.
10. Roux V, El Karkouri K, Lagier JC, Robert C, Raoult D. Non-contiguous finished genome sequence and description of Kurthia massiliensis sp. nov. Stand Genomic Sci 2012; 7:221-232. PubMed http://dx.doi.org/10.4056/sigs.3206554
11. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541-547. PubMed http://dx.doi.org/10.1038/nbt1360
12. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576-4579. PubMed http://dx.doi.org/10.1073/pnas.87.12.4576
13. Murray RGE. The Higher Taxa, or, a Place for Everything.? In: Holt JG (ed), Bergey's Manual of Systematic Bacteriology, First Edition, Volume 1, The Williams and Wilkins Co., Baltimore, 1984, p. 31-34.
14. Garrity GM, Holt JG. The Road Map to the Manual. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 119-169.
15. Gibbons NE, Murray RGE. Proposals Concerning the Higher Taxa of Bacteria. Int J Syst Bacteriol 1978; 28:1-6. http://dx.doi.org/10.1099/00207713-28-1-1
16. Ludwig W, Schleifer KH, Whitman WB. Class I. Bacilli class nov. In: De Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman WB (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 3, Springer-Verlag, New York, 2009, p. 19-20.
17. List of new names and new combinations previously effectively, but not validly, published. List no. 132. Int J Syst Evol Microbiol 2010; 60:469-472. http://dx.doi.org/10.1099/ijs.0.022855-0
18. Prévot AR. In: Hauderoy P, Ehringer G, Guillot G, Magrou. J., Prévot AR, Rosset D, Urbain A (eds), Dictionnaire des Bactéries Pathogènes, Second Edition, Masson et Cie, Paris, 1953, p. 1-692.
19. Skerman VBD, McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225-420. http://dx.doi.org/10.1099/00207713-30-1-225
20. Krasil'nikov NA. Guide to the Bacteria and Actinomycetes [Opredelitelv Bakterii i Actinomicetov], Akad. Nauk SSSR, Moscow, 1949, p. 328.
21. Keddie RM, Rogosa M. Genus Kurthia Trevisan 1885, 92; Nom. cons. Opin. 13, Jud. Comm. 1954, 152. In: Buchanan RE, Gibbons NE (eds), Bergey's Manual of Determinative Bacteriology, Eighth Edition, The Williams and Wilkins Co., Baltimore, 1974, p. 631-632.
22. Judicial Commission. Opinions 4, 6, 7, 8, 9, 10, 11, 12, 13, 14. Opinion 13. Int Bull Bacteriol Nomencl Taxon 1954; 4:141-158.
23. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000; 25:25-29. PubMed http://dx.doi.org/10.1038/75556
24. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol 2011; 28:2731-2739. PubMed http://dx.doi.org/10.1093/molbev/msr121
25. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152-155.
26. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128-130. http://dx.doi.org/10.1016/S0723-2020(11)80158-X
27. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199-202. http://dx.doi.org/10.1111/j.1574-6968.1990.tb03996.x
28. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911-917. PubMed http://dx.doi.org/10.1139/o59-099
29. Tindall BJ, Sikorski J, Smibert RM, Kreig NR. Phenotypic characterization and the principles of comparative systematics. In: Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM, Snyder LR (eds), Methods for General and Molecular Microbiology, 3rd edition, ASM Press, Washington, 2007, p. 330-393.
30. Schleifer KH. Analysis of the chemical composition and primary structure of murein. Methods Microbiol 1985; 18:123-156. http://dx.doi.org/10.1016/S0580-9517(08)70474-4
31. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407-477. PubMed
32. MacKenzie SL. Gas chromatography analysis of amino acids as the N-heptafluorobutyryl isobutyl esters. J Assoc Off Anal Chem 1987; 70:151-160. PubMed 33.http://www.dsmz.de/microorganisms/main.php?content
33. Prodigal http://prodigal.ornl.gov/ id=35.
34. GenBank database. http://www.ncbi.nlm.nih.gov/-genbank
35. Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000; 28:33-36. PubMed http://dx.doi.org/10.1093/nar/28.1.33
36. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955-964. PubMed http://dx.doi.org/10.1093/nar/25.5.0955
37. Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100-3108. PubMed http://dx.doi.org/10.1093/nar/gkm160
38. Krogh A, Larsson B, von Heijni G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001; 305:567-580. PubMed http://dx.doi.org/10.1006/jmbi.2000.4315
39. Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004; 340:783-795. PubMed http://dx.doi.org/10.1016/j.jmb.2004.05.028
40. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, et al. The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics 2008; 9:75-89. PubMed http://dx.doi.org/10.1186/1471-2164-9-75
41. Bose M, Barber RD. Prophage Finder: a prophage loci prediction tool for prokaryotic genome sequences. In Silico Biol 2006; 6:223-227. PubMed
42. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: a fast phage search tool. Nucleic Acids Res 2011; 39:W347-W352. PubMed http://dx.doi.org/10.1093/nar/gkr485
43. Nishida H. Evolution of genome base composition and genome size in bacteria. Front Microbiol 2012; 3:420. PubMed http://dx.doi.org/10.3389/fmicb.2012.00420